tbuckley/cabot-search huggingface dataset:
Explicit knowledge of task structure is a primary determinant of human model-based action
Authors: Pedro Castro-Rodrigues, Thomas Akam, Ivar Snorasson, Marta Camacho, Vitor Paixão, Ana Maia, J. Bernardo Barahona-Corrêa, Peter Dayan, H. Blair Simpson, Rui M. Costa, Albino J. Oliveira-Maia
Journal: Nature Human Behaviour (2022)
Machine learning model to predict mental health crises from electronic health records
Authors: Roger Garriga, Javier Mas, Semhar Abraha, Jon Nolan, Oliver Harrison, George Tadros, Aleksandar Matic
Journal: Nature Medicine (2022)

Abstract The timely identification of patients who are at risk of a mental health crisis can lead to improved outcomes and to the mitigation of burdens and costs. However, the high prevalence of mental health problems means that the manual review of complex patient records to make proactive care decisions is not feasible in practice. Therefore, we developed a machine learning model that uses electronic health records to continuously monitor patients for risk of a mental health crisis over a period of 28 days. The model achieves an area under the receiver operating characteristic curve of 0.797 and an area under the precision-recall curve of 0.159, predicting crises with a sensitivity of 58% at a specificity of 85%. A follow-up 6-month prospective study evaluated our algorithm’s use in clinical practice and observed predictions to be clinically valuable in terms of either managing caseloads or mitigating the risk of crisis in 64% of cases. To our knowledge, this study is the first to continuously predict the risk of a wide range of mental health crises and to explore the added value of such predictions in clinical practice.
Meta multi-task nuclei segmentation with fewer training samples
Authors: Chu Han, Huasheng Yao, Bingchao Zhao, Zhenhui Li, Zhenwei Shi, Lei Wu, Xin Chen, Jinrong Qu, Ke Zhao, Rushi Lan, Changhong Liang, Xipeng Pan, Zaiyi Liu
Journal: Medical Image Analysis (2022)
Self‐Delivering Nanodrugs Developed via Small‐Molecule‐Directed Assembly and Macrophage Cloaking for Sonodynamic‐Augmented Immunotherapy
Authors: Fang Xie, Zongjunlin Liu, Peiyuan Wang, Meimei Cai, Yang Li, Jianghua Yan, Qin Lin, Fanghong Luo
Journal: Advanced Healthcare Materials (2022)

Abstract The self‐delivery of sonosensitizers and immunomodulators to tumor areas, which is highly recommended for enhancing sonodynamic immunotherapy, remains a challenge. Herein, a self‐delivering nanodrug (HB‐NLG8189, drug loading: ≈100 wt%) is developed by the small‐molecule self‐assembly of "HB" (a new clinical photosensitizer) and NLG8189 (indoleamine‐(2,3)‐dioxygenase (IDO) pathway inhibitor) for sonodynamic‐augmented immunotherapy; this preparation method ensures the absence of excipient‐related toxicity and immunogenicity. To evade immune recognition and prolong the circulation time, the HB‐NLG8189 nanodrugs are camouflaged using macrophage cell membranes (MPCMs). The constructed HB‐NLG8189@MPCM nanodrugs show an ability to preferentially accumulate within tumors. Upon ultrasound triggering, the HB‐NLG8189@MPCM is able to generate reactive oxygen species efficiently for robust sonodynamic therapy; it induces immunogenic cell death, initiates an antitumor immune response to activate tumor‐specific effector T cells, and promotes the secretion of inflammatory cytokines. The concomitant delivery of NLG8189 reverses the immunosuppressive tumor microenvironment by restraining IDO‐1 activation and the intratumoral infiltration of regulatory T cells. Sonodynamic‐augmented immunotherapy with HB‐NLG8189@MPCM significantly inhibits the growth of both primary and distant tumors with little systemic toxicity. The biomimetic self‐delivery nanodrug provides a promising paradigm for improving sonodynamic immunotherapy.
Abstract A032: Integrating spatial analysis and agent-based modeling for studies of stroma sheltering effects in NSCLC
Authors: Tatiana Miti, Anna Miller, Daria Myroshnychenko, Bina Desai, Andriy Marusyk, David Basanta
Journal: Cancer Research (2022)

Abstract Background: Stroma plays a crucial role in shaping tumor growth dynamics, invasion, and metastasis. High stroma to tumor ratio in the clinic is associated with poor outcomes and shorter remission periods for lung cancer patients. Recent studies suggest that stroma shelters tumor cells during drug administration, but the precise mechanisms to confer this protection remain unclear. We hypothesize that stroma secretes paracrine factors that enhance tumor cells' proliferation rate in proximity, hence outcompeting the death rate due to therapies. In this context, the residual disease is an inherent stage in tumors' eco-evolutionary dynamics under treatment. Therefore, understanding the nature of stroma-tumor cell interactions is crucial for designing effective therapies. Methods: The spatial relationship between the stroma and proliferating tumor cells was interrogated via spatial analysis of 2D samples from mouse xenograft models and subsequent spatial agent-based modeling (ABM). Results: First, we built a pipeline to quantify the spatial extent and amplitude of stroma shielding the presence or absence of treatment. The spatial distributions of tumor cells, their proliferating rates, and the spatial extent of stroma protective effects are used to parametrize the ABM and simulate the spatio-temporal dynamics of tumor growth with and without treatment. Our preliminary results show moderately higher clustering of proliferating and stroma cells than stroma and non-proliferating cells or random distribution in the absence of treatment. In contrast, during therapy, stroma-proliferating tumor cell clustering is considerably higher than stroma-non proliferating tumor cells and stroma-random distribution. Moreover, stroma's protective effect during treatment seems limited to cells either in direct contact with stromal cells or in their immediate proximity. Conclusions: We expect our results to lead to novel therapeutic interventions that aim to shift eco-evolutionary dynamics rather than maximize short-term tumor cell killing efficiency. Citation Format: Tatiana Miti, Anna Miller, Daria Myroshnychenko, Bina Desai, Andriy Marusyk, David Basanta. Integrating spatial analysis and agent-based modeling for studies of stroma sheltering effects in NSCLC [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A032.
Trajectories and predictors of perinatal depressive symptoms among Kenyan women: a prospective cohort study
Authors: Anna Larsen, Jillian Pintye, Mary M Marwa, Salphine Watoyi, John Kinuthia, Felix Abuna, Barbra A Richardson, Laurén Gomez, Julia C Dettinger, Grace John-Stewart
Journal: The Lancet Psychiatry (2022)
A Sex-Adjusted Model for End-Stage Liver Disease Sodium Score for Equality in Liver Transplant
Authors: Brittany A. Shelton, Jayme E. Locke
Journal: JAMA Surgery (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Considerations for Use of Propensity Score Matching in Specific Patient Populations
Authors: Anne Goei, Tobias Kurth
Journal: JAMA Surgery (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Case 14-2022: A 57-Year-Old Man with Chylous Ascites
Authors: Michael Dougan, Mark A. Anderson, Jeremy S. Abramson, Megan J. Fitzpatrick
Journal: New England Journal of Medicine (2022)

A 57-year-old man was evaluated in the gastroenterology clinic because of new ascites. Paracentesis yielded milky-appearing ascitic fluid with a triglyceride level of 797 mg per deciliter. CT revealed multiple hypoenhancing liver lesions. There was a history of eosinophilic gastroenteritis and protein-losing enteropathy. A diagnostic test was performed.
Nanoparticle-delivered TLR4 and RIG-I agonists enhance immune response to SARS-CoV-2 subunit vaccine
Authors: Alexandra Atalis, Mark C. Keenum, Bhawana Pandey, Alexander Beach, Pallab Pradhan, Casey Vantucci, Laura O'Farrell, Richard Noel, Ritika Jain, Justin Hosten, Clinton Smith, Liana Kramer, Angela Jimenez, Miguel Armenta Ochoa, David Frey, Krishnendu Roy
Journal: Journal of Controlled Release (2022)
Comparison of Bayesian vs Frequentist Adaptive Trial Design in the Stroke Hyperglycemia Insulin Network Effort Trial
Authors: Kristine Broglio, William J. Meurer, Valerie Durkalski, Qi Pauls, Jason Connor, Donald Berry, Roger J. Lewis, Karen C. Johnston, William G. Barsan
Journal: JAMA Network Open (2022)

<h3>Importance</h3> Bayesian adaptive trial design has the potential to create more efficient clinical trials. However, a barrier to the uptake of bayesian adaptive designs for confirmatory trials is limited experience with how they may perform compared with a frequentist design. <h3>Objective</h3> To compare the performance of a bayesian and a frequentist adaptive clinical trial design. <h3>Design, Setting, and Participants</h3> This prospective cohort study compared 2 trial designs for a completed multicenter acute stroke trial conducted within a National Institutes of Health neurologic emergencies clinical trials network, with individual patient-level data, including the timing and order of enrollments and outcome ascertainment, from 1151 patients with acute stroke and hyperglycemia randomized to receive intensive or standard insulin therapy. The implemented frequentist design had group sequential boundaries for efficacy and futility interim analyses at 90 days after randomization for 500, 700, 900, and 1100 patients. The bayesian alternative used predictive probability of trial success to govern early termination for efficacy and futility with a first interim analysis at 500 randomized patients and subsequent interims after every 100 randomizations. <h3>Main Outcomes and Measures</h3> The main outcome was the sample size at end of study, which was defined as the sample size at which each of the studies stopped accrual of patients. <h3>Results</h3> Data were collected from 1151 patients. As conducted, the frequentist design passed the futility boundary after 936 participants were randomized. Using the same sequence and timing of randomization and outcome data, the bayesian alternative crossed the futility boundary approximately 3 months earlier after 800 participants were randomized. <h3>Conclusions and Relevance</h3> Both trial designs stopped for futility before reaching the planned maximum sample size. In both cases, the clinical community and patients would benefit from learning the answer to the trial's primary question earlier. The common feature across the 2 designs was frequent interim analyses to stop early for efficacy or for futility. Differences between how these analyses were implemented between the 2 trials resulted in the differences in early stopping.
The Oscillating Gut Microbiome and Its Effects on Host Circadian Biology
Authors: Lev Litichevskiy, Christoph A. Thaiss
Journal: Annual Review of Nutrition (2022)

The microbial community colonizing the gastrointestinal tract, collectively termed the gut microbiota, is an important element of the host organism due to its impact on multiple aspects of health. The digestion of food, secretion of immunostimulatory molecules, performance of chemical reactions in the intestine, and production of metabolites by the microbiota contribute to host homeostasis and disease. Recent discoveries indicate that these major functions are not constantly performed over the course of a day, but rather undergo diurnal fluctuations due to compositional and biogeographical oscillations in the microbiota. Here, we summarize the characteristics and origins of diurnal microbiome rhythms as well as their functional consequences for the circadian biology of the host. We describe the major known pathways of circadian host-microbiome communication and discuss possible implications of altered diurnal microbiome rhythms for human disease.
Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy
Authors: Cornelis J Boogerd, Grégory P A Lacraz, Ábel Vértesy, Sebastiaan J van Kampen, Ilaria Perini, Hesther de Ruiter, Danielle Versteeg, Andreas Brodehl, Petra van der Kraak, Mauro Giacca, Nicolaas de Jonge, Jan Philipp Junker, Alexander van Oudenaarden, Aryan Vink, Eva van Rooij
Journal: Cardiovascular Research (2022)

Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disorder that is characterized by progressive loss of myocardium that is replaced by fibro-fatty cells, arrhythmias, and sudden cardiac death. While myocardial degeneration and fibro-fatty replacement occur in specific locations, the underlying molecular changes remain poorly characterized. Here, we aim to delineate local changes in gene expression to identify new genes and pathways that are relevant for specific remodelling processes occurring during ACM.Using Tomo-Seq, genome-wide transcriptional profiling with high spatial resolution, we created transmural epicardial-to-endocardial gene expression atlases of explanted ACM hearts to gain molecular insights into disease-driving processes. This enabled us to link gene expression profiles to the different regional remodelling responses and allowed us to identify genes that are potentially relevant for disease progression. In doing so, we identified distinct gene expression profiles marking regions of cardiomyocyte degeneration and fibro-fatty remodelling and revealed Zinc finger and BTB domain-containing protein 11 (ZBTB11) to be specifically enriched at sites of active fibro-fatty replacement of myocardium. Immunohistochemistry indicated ZBTB11 to be induced in cardiomyocytes flanking fibro-fatty areas, which could be confirmed in multiple cardiomyopathy patients. Forced overexpression of ZBTB11 induced autophagy and cell death-related gene programmes in human cardiomyocytes, leading to increased apoptosis.Our study shows the power of Tomo-Seq to unveil new molecular mechanisms in human cardiomyopathy and uncovers ZBTB11 as a novel driver of cardiomyocyte loss.
Comment on Use of Biologic vs Synthetic Mesh for Single-stage Repair of Contaminated Ventral Hernias
Authors: Ozlem Boztepe, Giordano Perin, Saba Balasubramanian
Journal: JAMA Surgery (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Abstract IA019: Resolving the paradigm of the pre-existing resistance to targeted therapy, and the fitness costs associate with resistance: In vitro and theoretical evidence using an evolutionary game theoretic approach
Authors: Jacob G. Scott
Journal: Cancer Research (2022)

Abstract Therapeutic strategies for tumor control have traditionally assumed that maximizing reduction in tumor volume correlates with clinical efficacy. Unfortunately, this rapid decrease in tumor burden is almost invariably followed by the emergence of therapeutic resistance. Evolutionary based treatment strategies attempt to delay resistance via judicious treatments that maintain a significant treatable subpopulation. While these strategies have shown promise in recent clinical trials, they often rely on biological conjecture and intuition to derive parameters. To bridge this gap, we recently developed an in vitro assay to directly measure the parameters of the underlying evolutionary game played between cancer cells under therapy. Using this assay we have subsequently directly observed competitive exclusion in non-small cell lung cancer cells – a necessary, but not sufficient condition for adaptive therapy. Intrinsic to this finding lies another advance: one which helps us settle the long standing paradox of pre-existing resistance and fitness costs associated with resistance mutations. In particular, if a cost of resistance exists, how can a less fit mutant persist in a population long enough for a treatment to be given to expose its increased fitness? To answer this, we show experimental and theoretical results that help explain this paradox which we posit submit should be generalizable outside cancer and applicable across the kingdoms of life where eco-evolutionary dynamics are at play. Citation Format: Jacob G. Scott. Resolving the paradigm of the pre-existing resistance to targeted therapy, and the fitness costs associate with resistance: In vitro and theoretical evidence using an evolutionary game theoretic approach [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr IA019.
The absent/low expression of CD34 in NPM1-mutated AML is not related to cytoplasmic dislocation of NPM1 mutant protein
Authors: Giulia Pianigiani, Francesca Rocchio, Sara Peruzzi, Vibeke Andresen, Barbara Bigerna, Daniele Sorcini, Michela Capurro, Bjørn Tore Gjertsen, Paolo Sportoletti, Mauro Di Ianni, Maria Paola Martelli, Lorenzo Brunetti, Brunangelo Falini
Journal: Leukemia (2022)
Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish
Authors: Jaya Krishnan, Chris W. Seidel, Ning Zhang, Narendra Pratap Singh, Jake VanCampen, Robert Peuß, Shaolei Xiong, Alexander Kenzior, Hua Li, Joan W. Conaway, Nicolas Rohner
Journal: Nature Genetics (2022)
Adeno-associated-virus-mediated gene delivery to ovaries restores fertility in congenital infertile mice
Authors: Mito Kanatsu-Shinohara, Jiyoung Lee, Takehiro Miyazaki, Hiroko Morimoto, Takashi Shinohara
Journal: Cell Reports Medicine (2022)

Oocytes and granulosa cells closely interact with each other during follicular development, and a lack of appropriate signaling between them results in infertility. Attempts to manipulate oocyte microenvironment have been impeded by the impermeability of the blood-follicle barrier (BFB). To establish a strategy for manipulating oogenesis, we use adeno-associated viruses (AAVs), which have a unique ability of transcytosis. Microinjecting of AAVs into the ovarian stroma penetrates the BFB and achieves long-term gene expression. Introduction of an AAV carrying the mouse Kitl gene restores oogenesis in congenitally infertile KitlSl-t/KitlSl-t mutant mouse ovaries, which lack Kitl expression but contain only primordial follicles. Healthy offspring without AAV integration are born by natural mating. Therefore, AAV-mediated gene delivery not only provides a means for studying oocyte-granulosa interactions through the manipulation of the oocyte microenvironment but could also be a powerful method to treat female infertility resulting from somatic cell defects.
<i>QuickStats:</i> Percentage of Suicides* and Homicides† Involving a Firearm Among Persons Aged ≥10 Years, by Age Group — National Vital Statistics System, United States, 2020§
Journal: MMWR Morbidity and Mortality Weekly Report (2022)

Cause of deathHomicidePercentage 10-24 yrs 25-44 yrs 45-64 yrs ≥65 yrs Abbreviation: ICD-10 = International Classification of Diseases, Tenth Revision.* Suicide was identified using ICD-10 underlying cause-of-death codes U03, X60-X84, and Y87.0.Firearminvolved suicide was identified using ICD-10 underlying cause-of-death codes X72-X74.† Homicide was identified using ICD-10 underlying cause-of-death codes U01-U02, X85-Y09, and Y87.1.Firearminvolved homicide was identified using ICD-10 underlying cause-of-death codes U01.4 and X93-X95.§ In 2020, approximately 8 in 10 homicides and 5 in 10 suicides in the United States involved firearms.Additional information on firearm homicide and firearm suicide rates during 2019-2020 is available at https://www.cdc.gov/mmwr/volumes/71/wr/mm7119e1.htmIn 2020, among persons aged ≥10 years, the percentage of suicide deaths that involved a firearm was lowest among those aged 25-44 years (45.1%) and highest among those aged ≥65 years (70.8%).The percentage of homicide deaths that involved a firearm decreased with age, from 91.6% among those aged 10-24 years to 46.0% among those aged ≥65 years.Persons aged ≥65 years had the highest percentage of suicide deaths that involved a firearm but the lowest percentage of homicide deaths that involved a firearm.